[adegenet-forum] conversion genind to loci

[Thibaut Jombart]

Hi there,

as this question is also pegas-related, it may be better suited on 
R-sig-genetics (I am not sure Emmanuel Paradis reads the adegenet forum):
https://stat.ethz.ch/mailman/listinfo/r-sig-genetics

This list was typically a bit of a deadland but we are trying to 
resurrect it.

Cheers
Thibaut

On 06/04/15 14:48, Virgilio Massimiliano wrote:
> hi,
> I’m trying to make a bootstrapped njt on msat data,
> as far as I can understand, it’s not possible to bootstrap my loci 
> starting from a genind object and this:
>
> myBoots <- boot.phylo(NJtree, data_genind at tab, B =100, function(xx) 
>  njs(dist(xx)))
>
> shouldn’t be correct as it bootstraps alleles (data_genind at tab)
>
>
> So I’m trying to convert my genind data into loci using genind2loci 
> and read.loci :
>
>
> library(adegenet)
> data <- read.genetix("data.gtx")
> data_loci<-genind2loci(data)
> write.csv(data_loci, file = "data_loci.csv")
> library(pegas)
> data_pegas<-read.loci(file = "data_loci.csv", loci.sep = ",")
>
> and then get the tree (based on Fst, but it doesn’t work either with 
> distances)
>
> pairFst <- pairwise.fst(data, res.type="matrix", truenames=TRUE)
>
> library(ape)
> njtreFst_pop <- njs(pairFst)
> myBoots <- boot.phylo(njtreFst_pop, as.matrix(data_pegas), B = 3, 
> function(xx)
>   njs(dist(xx)))
>
> but it doesn’t seem to work (I’m attaching the input file) and I get 
> only error messages no matter what I try...
>
> What am I doing wrong? Is there a simpler way of getting bootstrapped 
> msat loci starting form a genind object?
>
> greeting and many thanks in advance
>
> Massi
>
>
>
> __________________________________
>  Massimiliano Virgilio, PhD
>
> Royal Museum for Central Africa
>
> Joint Experimental Molecular Unit (JEMU)
>
> Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366
>
> massimiliano.virgilio at africamuseum.be 
> <mailto:massimiliano.virgilio at africamuseum.be>
>
> http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/
>
> http://jemu.myspecies.info
>
>
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